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Bárcenas-López DA, Mendiola-Soto DK, Núñez-Enríquez JC, Mejía-Aranguré JM, Hidalgo-Miranda A, Jiménez-Morales S. Promising genes and variants to reduce chemotherapy adverse effects in acute lymphoblastic leukemia. Transl Oncol 2021; 14:100978. [PMID: 33290991 PMCID: PMC7720095 DOI: 10.1016/j.tranon.2020.100978] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 11/17/2020] [Accepted: 11/25/2020] [Indexed: 12/12/2022] Open
Abstract
Almost two decades ago, the sequencing of the human genome and high throughput technologies came to revolutionize the clinical and therapeutic approaches of patients with complex human diseases. In acute lymphoblastic leukemia (ALL), the most frequent childhood malignancy, these technologies have enabled to characterize the genomic landscape of the disease and have significantly improved the survival rates of ALL patients. Despite this, adverse reactions from treatment such as toxicity, drug resistance and secondary tumors formation are still serious consequences of chemotherapy, and the main obstacles to reduce ALL-related mortality. It is well known that germline variants and somatic mutations in genes involved in drug metabolism impact the efficacy of drugs used in oncohematological diseases therapy. So far, a broader spectrum of clinically actionable alterations that seems to be crucial for the progression and treatment response have been identified. Although these results are promising, it is necessary to put this knowledge into the clinics to help physician make medical decisions and generate an impact in patients' health. This review summarizes the gene variants and clinically actionable mutations that modify the efficacy of antileukemic drugs. Therefore, knowing their genetic status before treatment is critical to reduce severe adverse effects, toxicities and life-threatening consequences in ALL patients.
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Affiliation(s)
- Diego Alberto Bárcenas-López
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica, Periferico Sur 4809, Arenal Tepepan, Del. Tlalpan, Mexico City 14610, Mexico; Programa de Doctorado, Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Diana Karen Mendiola-Soto
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica, Periferico Sur 4809, Arenal Tepepan, Del. Tlalpan, Mexico City 14610, Mexico; Programa de Doctorado en Ciencias Biomédicas, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Juan Carlos Núñez-Enríquez
- Unidad de Investigación Médica en Epidemiología Clínica, Hospital de Pediatría, CMNSXXI, Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | - Juan Manuel Mejía-Aranguré
- Unidad de Investigación Médica en Epidemiología Clínica, Hospital de Pediatría, CMNSXXI, Instituto Mexicano del Seguro Social, Mexico City, Mexico; Coordinación de Investigación en Salud, Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | - Alfredo Hidalgo-Miranda
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica, Periferico Sur 4809, Arenal Tepepan, Del. Tlalpan, Mexico City 14610, Mexico
| | - Silvia Jiménez-Morales
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica, Periferico Sur 4809, Arenal Tepepan, Del. Tlalpan, Mexico City 14610, Mexico.
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2
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Barz MJ, Hof J, Groeneveld-Krentz S, Loh JW, Szymansky A, Astrahantseff K, von Stackelberg A, Khiabanian H, Ferrando AA, Eckert C, Kirschner-Schwabe R. Subclonal NT5C2 mutations are associated with poor outcomes after relapse of pediatric acute lymphoblastic leukemia. Blood 2020; 135:921-933. [PMID: 31971569 PMCID: PMC7218751 DOI: 10.1182/blood.2019002499] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Accepted: 12/28/2019] [Indexed: 12/27/2022] Open
Abstract
Activating mutations in cytosolic 5'-nucleotidase II (NT5C2) are considered to drive relapse formation in acute lymphoblastic leukemia (ALL) by conferring purine analog resistance. To examine the clinical effects of NT5C2 mutations in relapsed ALL, we analyzed NT5C2 in 455 relapsed B-cell precursor ALL patients treated within the ALL-REZ BFM 2002 relapse trial using sequencing and sensitive allele-specific real-time polymerase chain reaction. We detected 110 NT5C2 mutations in 75 (16.5%) of 455 B-cell precursor ALL relapses. Two-thirds of relapses harbored subclonal mutations and only one-third harbored clonal mutations. Event-free survival after relapse was inferior in patients with relapses with clonal and subclonal NT5C2 mutations compared with those without (19% and 25% vs 53%, P < .001). However, subclonal, but not clonal, NT5C2 mutations were associated with reduced event-free survival in multivariable analysis (hazard ratio, 1.89; 95% confidence interval, 1.28-2.69; P = .001) and with an increased rate of nonresponse to relapse treatment (subclonal 32%, clonal 12%, wild type 9%, P < .001). Nevertheless, 27 (82%) of 33 subclonal NT5C2 mutations became undetectable at the time of nonresponse or second relapse, and in 10 (71%) of 14 patients subclonal NT5C2 mutations were undetectable already after relapse induction treatment. These results show that subclonal NT5C2 mutations define relapses associated with high risk of treatment failure in patients and at the same time emphasize that their role in outcome is complex and goes beyond mutant NT5C2 acting as a targetable driver during relapse progression. Sensitive, prospective identification of NT5C2 mutations is warranted to improve the understanding and treatment of this aggressive ALL relapse subtype.
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Affiliation(s)
- Malwine J Barz
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin-Berlin Institute of Health, Berlin, Germany
| | - Jana Hof
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin-Berlin Institute of Health, Berlin, Germany
| | - Stefanie Groeneveld-Krentz
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin-Berlin Institute of Health, Berlin, Germany
| | - Jui Wan Loh
- Rutgers Cancer Institute of New Jersey, Rutgers University, New Brunswick, NJ
- Graduate Program in Microbiology and Molecular Genetics, Rutgers University, Piscataway, NJ
| | - Annabell Szymansky
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin-Berlin Institute of Health, Berlin, Germany
- Institute of Biology, Freie Universität Berlin, Berlin, Germany
| | - Kathy Astrahantseff
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin-Berlin Institute of Health, Berlin, Germany
| | - Arend von Stackelberg
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin-Berlin Institute of Health, Berlin, Germany
| | - Hossein Khiabanian
- Rutgers Cancer Institute of New Jersey, Rutgers University, New Brunswick, NJ
- Graduate Program in Microbiology and Molecular Genetics, Rutgers University, Piscataway, NJ
- Department of Pathology and Laboratory Medicine, Rutgers Robert Wood Johnson Medical School, Rutgers University, New Brunswick, NJ
| | - Adolfo A Ferrando
- Institute of Cancer Genetics, Columbia University, New York, NY; and
| | - Cornelia Eckert
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin-Berlin Institute of Health, Berlin, Germany
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Renate Kirschner-Schwabe
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin-Berlin Institute of Health, Berlin, Germany
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany
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3
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Moriyama T, Liu S, Li J, Meyer J, Zhao X, Yang W, Shao Y, Heath R, Hnízda A, Carroll WL, Yang JJ. Mechanisms of NT5C2-Mediated Thiopurine Resistance in Acute Lymphoblastic Leukemia. Mol Cancer Ther 2019; 18:1887-1895. [PMID: 31358663 DOI: 10.1158/1535-7163.mct-18-1112] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Revised: 02/15/2019] [Accepted: 07/23/2019] [Indexed: 02/02/2023]
Abstract
Relapse remains a formidable challenge for acute lymphoblastic leukemia (ALL). Recently, recurrent mutations in NT5C2 were identified as a common genomic lesion unique in relapsed ALL and were linked to acquired thiopurine resistance. However, molecular mechanisms by which NT5C2 regulates thiopurine cytotoxicity were incompletely understood. To this end, we sought to comprehensively characterize the biochemical and cellular effects of NT5C2 mutations. Compared with wild-type NT5C2, mutant proteins showed elevated 5'-nucleotidase activity with a stark preference of thiopurine metabolites over endogenous purine nucleotides, suggesting neomorphic effects specific to thiopurine metabolism. Expression of mutant NT5C2 mutations also significantly reduced thiopurine uptake in vitro with concomitant increase in efflux of 6-mercaptopurine (MP) metabolites, plausibly via indirect effects on drug transporter pathways. Finally, intracellular metabolomic profiling revealed significant shifts in nucleotide homeostasis induced by mutant NT5C2 at baseline; MP treatment also resulted in global changes in metabolomic profiles with completely divergent effects in cells with mutant versus wild-type NT5C2. Collectively, our data indicated that NT5C2 mutations alter thiopurine metabolism and cellular disposition, but also influence endogenous nucleotide homeostasis and thiopurine-induced metabolomic response. These complex mechanisms contributed to NT5C2-mediated drug resistance in ALL and pointed to potential opportunities for therapeutic targeting in relapsed ALL.
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Affiliation(s)
- Takaya Moriyama
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee.
| | - Shuguang Liu
- Hematology Oncology Center, Beijing Children's Hospital, Capital Medical University, Beijing, China
| | - Jing Li
- Department of Oncology, Pharmacology Core, Karmanos Cancer Institute, Wayne State University School of Medicine, Detroit, Michigan
| | - Julia Meyer
- Department of Pediatrics, Benioff Children's Hospital, University of California, San Francisco, California
| | - Xujie Zhao
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Wentao Yang
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Youming Shao
- Protein Production Center, St. Jude Children's Hospital, Memphis, Tennessee
| | - Richard Heath
- Protein Production Center, St. Jude Children's Hospital, Memphis, Tennessee
| | - Aleš Hnízda
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - William L Carroll
- New York University Cancer Institute, New York University Langone Medical Center, New York, New York.,Department of Pathology, New York University Langone Medical Center, New York, New York.,Department of Pediatrics, New York University Langone Medical Center, New York, New York
| | - Jun J Yang
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee. .,Department of Oncology, St. Jude Children's Research Hospital, Memphis, Tennessee
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Man P, Fábry M, Sieglová I, Kavan D, Novák P, Hnízda A. Thiopurine intolerance-causing mutations in NUDT15 induce temperature-dependent destabilization of the catalytic site. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2019; 1867:376-381. [PMID: 30639426 DOI: 10.1016/j.bbapap.2019.01.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Revised: 12/16/2018] [Accepted: 01/06/2019] [Indexed: 01/18/2023]
Abstract
Germline mutations in NUDT15 cause thiopurine intolerance during treatment of leukemia or autoimmune diseases. Previously, it has been shown that the mutations affect the enzymatic activity of the NUDT15 hydrolase due to decreased protein stability in vivo. Here we provide structural insights into protein destabilization in R139C and V18I mutants using thermolysin-based proteolysis and H/D exchange followed by mass spectrometry. Both mutants exhibited destabilization of the catalytic site, which was more pronounced at higher temperature. This structural perturbation is shared by the mutations despite their different positions within the protein structure. Reaction products of NUDT15 reverted these conformational abnormalities, demonstrating the importance of ligands for stabilization of a native state of the mutants. This study shows the action of pharmacogenetic variants in NUDT15 in a context of protein structure, which might open novel directions in personalized chemotherapy.
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Affiliation(s)
- Petr Man
- Institute of Microbiology, Academy of Sciences of the Czech Republic, Videnska 1083, Prague 4 142 20, Czech Republic; Faculty of Science, Charles University, Hlavova 2030/8, Prague 2 128 43, Czech Republic
| | - Milan Fábry
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Videnska 1083, Prague 4 142 20, Czech Republic
| | - Irena Sieglová
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Videnska 1083, Prague 4 142 20, Czech Republic; Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nam. 2, Prague 6 166 10, Czech Republic
| | - Daniel Kavan
- Institute of Microbiology, Academy of Sciences of the Czech Republic, Videnska 1083, Prague 4 142 20, Czech Republic; Faculty of Science, Charles University, Hlavova 2030/8, Prague 2 128 43, Czech Republic
| | - Petr Novák
- Institute of Microbiology, Academy of Sciences of the Czech Republic, Videnska 1083, Prague 4 142 20, Czech Republic; Faculty of Science, Charles University, Hlavova 2030/8, Prague 2 128 43, Czech Republic
| | - Aleš Hnízda
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nam. 2, Prague 6 166 10, Czech Republic.
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5
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Towards personalized chemotherapy of acute lymphoblastic leukemia. Oncotarget 2018; 9:36728-36729. [PMID: 30613359 PMCID: PMC6298412 DOI: 10.18632/oncotarget.26420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Accepted: 11/26/2018] [Indexed: 11/25/2022] Open
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Dieck CL, Tzoneva G, Forouhar F, Carpenter Z, Ambesi-Impiombato A, Sánchez-Martín M, Kirschner-Schwabe R, Lew S, Seetharaman J, Tong L, Ferrando AA. Structure and Mechanisms of NT5C2 Mutations Driving Thiopurine Resistance in Relapsed Lymphoblastic Leukemia. Cancer Cell 2018; 34:136-147.e6. [PMID: 29990496 PMCID: PMC6049837 DOI: 10.1016/j.ccell.2018.06.003] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Revised: 04/06/2018] [Accepted: 06/06/2018] [Indexed: 11/25/2022]
Abstract
Activating mutations in the cytosolic 5'-nucleotidase II gene NT5C2 drive resistance to 6-mercaptopurine in acute lymphoblastic leukemia. Here we demonstrate that constitutively active NT5C2 mutations K359Q and L375F reconfigure the catalytic center for substrate access and catalysis in the absence of allosteric activator. In contrast, most relapse-associated mutations, which involve the arm segment and residues along the surface of the inter-monomeric cavity, disrupt a built-in switch-off mechanism responsible for turning off NT5C2. In addition, we show that the C-terminal acidic tail lost in the Q523X mutation functions to restrain NT5C2 activation. These results uncover dynamic mechanisms of enzyme regulation targeted by chemotherapy resistance-driving NT5C2 mutations, with important implications for the development of NT5C2 inhibitor therapies.
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Affiliation(s)
- Chelsea L Dieck
- Institute for Cancer Genetics, Columbia University, New York, NY 10032, USA
| | - Gannie Tzoneva
- Institute for Cancer Genetics, Columbia University, New York, NY 10032, USA
| | - Farhad Forouhar
- Hervert Irving Comprehensive Cancer Center, Columbia University, New York, NY 10032, USA; Department of Biological Sciences, Northeast Structural Genomics Consortium, Columbia University, 1212 Amsterdam Avenue, 701 Fairchild Center, New York, NY 10027, USA
| | - Zachary Carpenter
- Department of Systems Biology, Columbia University, New York, NY 10032, USA
| | | | | | - Renate Kirschner-Schwabe
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin 10117, Germany
| | - Scott Lew
- Department of Biological Sciences, Northeast Structural Genomics Consortium, Columbia University, 1212 Amsterdam Avenue, 701 Fairchild Center, New York, NY 10027, USA
| | | | - Liang Tong
- Department of Biological Sciences, Northeast Structural Genomics Consortium, Columbia University, 1212 Amsterdam Avenue, 701 Fairchild Center, New York, NY 10027, USA.
| | - Adolfo A Ferrando
- Institute for Cancer Genetics, Columbia University, New York, NY 10032, USA; Department of Systems Biology, Columbia University, New York, NY 10032, USA; Department of Pediatrics, Columbia University Medical Center, 1130 St. Nicholas Avenue, ICRC 402, New York, NY 10032, USA; Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY 10032, USA.
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7
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Hnízda A, Fábry M, Moriyama T, Pachl P, Kugler M, Brinsa V, Ascher DB, Carroll WL, Novák P, Žaliová M, Trka J, Řezáčová P, Yang JJ, Veverka V. Relapsed acute lymphoblastic leukemia-specific mutations in NT5C2 cluster into hotspots driving intersubunit stimulation. Leukemia 2018. [PMID: 29535428 DOI: 10.1038/s41375-018-0073-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Activating mutations in NT5C2, a gene encoding cytosolic purine 5'-nucleotidase (cN-II), confer chemoresistance in relapsed acute lymphoblastic leukemia. Here we show that all mutants became independent of allosteric effects of ATP and thus constitutively active. Structural mapping of mutations described in patients demonstrates that 90% of leukemia-specific allelles directly affect two regulatory hotspots within the cN-II molecule-the helix A region: residues 355-365, and the intersubunit interface: helix B (232-242) and flexible interhelical loop L (400-418). Furthermore, analysis of hetero-oligomeric complexes combining wild-type (WT) and mutant subunits showed that the activation is transmitted from the mutated to the WT subunit. This intersubunit interaction forms structural basis of hyperactive NT5C2 in drug-resistant leukemia in which heterozygous NT5C2 mutation gave rise to hetero-tetramer mutant and WT proteins. This enabled us to define criteria to aid the prediction of NT5C2 drug resistance mutations in leukemia.
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Affiliation(s)
- Aleš Hnízda
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nam. 2, Prague 6, 166 10, Czech Republic. .,Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, UK.
| | - Milan Fábry
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Videnska 1083, Prague 4, 142 20, Czech Republic
| | - Takaya Moriyama
- Department of Pharmaceutical Sciences, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Petr Pachl
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nam. 2, Prague 6, 166 10, Czech Republic
| | - Michael Kugler
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nam. 2, Prague 6, 166 10, Czech Republic.,Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Videnska 1083, Prague 4, 142 20, Czech Republic
| | - Vítězslav Brinsa
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nam. 2, Prague 6, 166 10, Czech Republic
| | - David B Ascher
- Department of Biochemistry, Sanger Building, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK.,Department of Biochemistry and Molecular Biology, Bio21 Institute, University of Melbourne, 30 Flemington Road, Parkville, VIC, 3052, Australia
| | | | - Petr Novák
- Institute of Microbiology, Academy of Sciences of the Czech Republic, Videnska 1083, Prague, 4 142 20, Czech Republic
| | - Markéta Žaliová
- Childhood Leukaemia Investigation Prague, Department of Paediatric Haematology and Oncology, Second Faculty of Medicine, Charles University and University Hospital Motol, Prague, Czech Republic
| | - Jan Trka
- Childhood Leukaemia Investigation Prague, Department of Paediatric Haematology and Oncology, Second Faculty of Medicine, Charles University and University Hospital Motol, Prague, Czech Republic
| | - Pavlína Řezáčová
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nam. 2, Prague 6, 166 10, Czech Republic.,Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Videnska 1083, Prague 4, 142 20, Czech Republic
| | - Jun J Yang
- Department of Pharmaceutical Sciences, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Václav Veverka
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nam. 2, Prague 6, 166 10, Czech Republic
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